PDBsum entry 1yht

Hydrolase

PDB id: 1yht

Contents

Protein chain

344 a.a. *

Ligands

ACY

GOL ×2

Waters ×243

* Residue conservation analysis

PDB id:

1yht

Name:

Hydrolase

Title:

Crystal structure analysis of dispersin b

Structure:

Dspb. Chain: a. Engineered: yes

Source:

Aggregatibacter actinomycetemcomitans. Organism_taxid: 714. Strain: cu1000. Gene: dspb. Expressed in: escherichia coli. Expression_system_taxid: 562.

Resolution:

2.00Å R-factor: 0.154 R-free: 0.211

Authors:

N.Ramasubbu,L.M.Thomas,C.Ragunath,J.B.Kaplan

Key ref:

N.Ramasubbu et al. (2005). Structural analysis of dispersin B, a biofilm-releasing glycoside hydrolase from the periodontopathogen Actinobacillus actinomycetemcomitans. J Mol Biol, 349, 475-486. PubMed id: 15878175 DOI: 10.1016/j.jmb.2005.03.082

Date:

10-Jan-05 Release date: 10-Jan-06

Protein chain

Q840G9  (Q840G9_AGGAC) -  DspB (Fragment) from Aggregatibacter actinomycetemcomitans

Seq: 361 a.a.

Struc: 344 a.a.

Enzyme reactions

• Enzyme class: E.C.3.2.1.52 - beta-N-acetylhexosaminidase.
• Reaction: Hydrolysis of terminal non-reducing N-acetyl-D-hexosamine residues in N-acetyl-beta-D-hexosaminides.

DOI no: 10.1016/j.jmb.2005.03.082

J Mol Biol 349:475-486 (2005)

PubMed id: 15878175

Structural analysis of dispersin B, a biofilm-releasing glycoside hydrolase from the periodontopathogen Actinobacillus actinomycetemcomitans.

N.Ramasubbu, L.M.Thomas, C.Ragunath, J.B.Kaplan.

ABSTRACT

Bacteria in a biofilm are enmeshed in a self-synthesized extracellular polysaccharide matrix that holds the bacteria together in a mass and firmly attaches the bacterial mass to the underlying surface. A major component of the extracellular polysaccharide matrix in several phylogenetically diverse bacteria is PGA, a linear polymer of N-acetylglucosamine residues in beta(1,6)-linkage. PGA is produced by the Gram-negative periodontopathogen Actinobacillus actinomycetemcomitans as well as by the Gram-positive device-associated pathogen Staphylococcus epidermidis. We recently reported that A.actinomycetemcomitans produces a soluble glycoside hydrolase named dispersin B, which degrades PGA. Here, we present the crystal structure of dispersin B at 2.0A in complex with a glycerol and an acetate ion at the active site. The enzyme crystallizes in the orthorhombic space group C222(1) with cell dimensions a=41.02A, b=86.13A, c=185.77A. The core of the enzyme consists a (beta/alpha)(8) barrel topology similar to other beta-hexosaminidases but significant differences exist in the arrangement of loops hovering in the vicinity of the active site. The location and interactions of the glycerol and acetate moieties in conjunction with the sequence analysis suggest that dispersin B cleaves beta(1,6)-linked N-acetylglucosamine polymer using a catalytic machinery similar to other family 20 hexosaminidases which cleave beta(1,4)-linked N-acetylglucosamine residues.

Selected figure(s)

Figure 2.
Figure 2. The topology and comparison with the homologues of DspB. (a) Schematic topogram generated by the program TOPS located at the URL (http://www.tops.leeds.ac.uk/). a-Helices are represented by cylinders and b-strands by arrows. (b) Ribbon diagram for the refined structure of DspB showing the TIM barrel down the barrel axis. (c) A 2F[o] -F[c] difference density map around the putative active site. The map is contoured at 1.5s. The refined model of DspB has been superimposed. (d) Superposition of 1HP5 (green) and DspB (magenta) by least-squares fit as derived from the program SPDBV (http://www.expasy.org/spdbv/).

Figure 4.
Figure 4. Diagrammatic illustration of the interactions formed by the ligands bound in the active sites of DspB (a) and 1HP5 (b). The hydrogen bond interactions are indicated with a broken line. An arc with radiating lines represents the hydrophobic interactions in the structure. The glycerol is labeled as Gol. (c) Superposition of active site residues at subsite -1 of 1HP5 (magenta) with the corresponding residue from DspB (green). Note that the residues in both the enzymes are almost conserved. Note also the absence of the Trp408 residue in DspB and the difference in the loop conformation and length in DspB.

The above figures are reprinted by permission from Elsevier: J Mol Biol (2005, 349, 475-486) copyright 2005.

Figures were selected by an automated process.